Search results for: full genome sequencing

Authors: Junus Mara, Herman Parung, Jhony Tanijaya, Rudy Djamaluddin

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The purpose of this study is to determine the behavior of beam-column sub-assemblages castella due to cyclic loading. Knowing these behaviors can if be analyzed the effectiveness of the concrete filler to reduce the damage and improve capacity of beam castella. Test beam consists of beam castella fabricated from normal beam (CB), castella beams with concrete filler between the flange (CCB) and normal beam (NB) as a comparison. Results showed castella beam (CB) has the advantage to increase the flexural capacity and energy absorption respectively 100.5% and 74.3%. Besides advantages, castella beam has the disadvantage that lowering partial ductility and full ductility respectively 12.6% and 18.1%, decrease resistance ratio 29.5% and accelerate the degradation rate of stiffness ratio 31.4%. By the concrete filler between the beam flange to improve the ability of castella beam, then the beam castella have the ability to increase the flexural capacity of 184.78 %, 217.1% increase energy absorption, increase ductility partial and full ductility respectively 27.9 % and 26 %, increases resistance ratio 52.5% and slow the rate of degradation of the stiffness ratio 55.1 %.

Keywords: steel, castella, column beams, cyclic load

Procedia PDF Downloads 434

Authors: Hanbyul Kim, Hye-Jin Kin, Taehun Park, Woo Jun Sul, Susun An

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Skin is the largest organ of the human body and can provide the diverse habitat for various microorganisms. The ecology of the skin surface selects distinctive sets of microorganisms and is influenced by both endogenous intrinsic factors and exogenous environmental factors. The diversity of the bacterial community in the skin also depends on multiple host factors: gender, age, health status, location. Among them, age-related changes in skin structure and function are attributable to combinations of endogenous intrinsic factors and exogenous environmental factors. Skin aging is characterized by a decrease in sweat, sebum and the immune functions thus resulting in significant alterations in skin surface physiology including pH, lipid composition, and sebum secretion. The present study gives a comprehensive clue on the variation of skin microbiota and the correlations between ages by analyzing and comparing the metagenome of skin microbiome using Next Generation Sequencing method. Skin bacterial diversity and composition were characterized and compared between two different age groups: younger (20 – 30y) and older (60 - 70y) Xian, Chinese women. A total of 73 healthy women meet two conditions: (I) living in Xian, China; (II) maintaining healthy skin status during the period of this study. Based on Ribosomal Database Project (RDP) database, skin samples of 73 participants were enclosed with ten most abundant genera: Chryseobacterium, Propionibacterium, Enhydrobacter, Staphylococcus and so on. Although these genera are the most predominant genus overall, each genus showed different proportion in each group. The most dominant genus, Chryseobacterium was more present relatively in Young group than in an old group. Similarly, Propionibacterium and Enhydrobacter occupied a higher proportion of skin bacterial composition of the young group. Staphylococcus, in contrast, inhabited more in the old group. The beta diversity that represents the ratio between regional and local species diversity showed significantly different between two age groups. Likewise, The Principal Coordinate Analysis (PCoA) values representing each phylogenetic distance in the two-dimensional framework using the OTU (Operational taxonomic unit) values of the samples also showed differences between the two groups. Thus, our data suggested that the composition and diversification of skin microbiomes in adult women were largely affected by chronological and physiological skin aging.

Keywords: next generation sequencing, age, Xian, skin microbiome

Procedia PDF Downloads 135

Authors: Stepan Papacek, Jiri Jablonsky, Radek Kana, Ctirad Matonoha, Stefan Kindermann

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FRAP (Fluorescence Recovery After Photobleaching) is a widely used measurement technique to determine the mobility of fluorescent molecules within living cells. While the experimental setup and protocol for FRAP experiments are usually fixed, data processing part is still under development. In this paper, we formulate and solve the problem of data selection which enhances the processing of FRAP images. We introduce the concept of the irrelevant data set, i.e., the data which are almost not reducing the confidence interval of the estimated parameters and thus could be neglected. Based on sensitivity analysis, we both solve the problem of the optimal data space selection and we find specific conditions for optimizing an important experimental design factor, e.g., the radius of bleach spot. Finally, a theorem announcing less precision of the integrated data approach compared to the full data case is proven; i.e., we claim that the data set represented by the FRAP recovery curve lead to a larger confidence interval compared to the spatio-temporal (full) data.

Keywords: FRAP, inverse problem, parameter identification, sensitivity analysis, optimal experimental design

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Authors: Laaziz El Hassan

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The Service Network Design Problem (SNDP) is a tactical issue in freight transportation firms. The existing formulations of the problem for intermodal rail-road transportation were not always adapted to the intermodality in terms of full asset utilization and modal shift reinforcement. The objective of the article is to propose a model having a more compliant formulation with intermodality, including constraints highlighting the imperatives of asset management, reinforcing modal shift from road to rail and reducing, by the way, road mode CO2 emissions. The model is a fixed charged, path based integer nonlinear program. Its objective is to minimize services total cost while ensuring full assets utilization to satisfy freight demand forecast. The model's main feature is that it gives as output both the train sizes and the services frequencies for a planning period. We solved the program using a commercial solver and discussed the numerical results.

Keywords: intermodal transport network, service network design, model, nonlinear integer program, path-based, service frequencies, modal shift

Procedia PDF Downloads 101

Authors: Alexander Goncharenko, Andrey Denisov, Sergey Alyamkin, Evgeny Terentev

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The neural network quantization is highly desired procedure to perform before running neural networks on mobile devices. Quantization without fine-tuning leads to accuracy drop of the model, whereas commonly used training with quantization is done on the full set of the labeled data and therefore is both time- and resource-consuming. Real life applications require simplification and acceleration of quantization procedure that will maintain accuracy of full-precision neural network, especially for modern mobile neural network architectures like Mobilenet-v1, MobileNet-v2 and MNAS. Here we present a method to significantly optimize training with quantization procedure by introducing the trained scale factors for discretization thresholds that are separate for each filter. Using the proposed technique, we quantize the modern mobile architectures of neural networks with the set of train data of only ∼ 10% of the total ImageNet 2012 sample. Such reduction of train dataset size and small number of trainable parameters allow to fine-tune the network for several hours while maintaining the high accuracy of quantized model (accuracy drop was less than 0.5%). Ready-for-use models and code are available in the GitHub repository.

Keywords: distillation, machine learning, neural networks, quantization

Procedia PDF Downloads 298

Authors: Xiaoyun Zhao, Rami Darwish, Anna Pernestål

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Automated vehicles (AVs) have the potential to enhance road capacity, improving road safety and traffic efficiency. Research and development on AVs have been going on for many years. However, when the complicated traffic rules and real situations interacted, AVs fail to make decisions on contradicting situations, and are not able to have control in all conditions due to highly dynamic driving scenarios. This limits AVs’ usage and restricts the full potential benefits that they can bring. Furthermore, regulations, infrastructure development, and public acceptance cannot keep up at the same pace as technology breakthroughs. Facing these challenges, this paper proposes automated vehicle traffic control tower (AVTCT) acting as a safe, efficient and integrated solution for AV control. It introduces a concept of AVTCT for control, management, decision-making, communication and interaction with various aspects in transportation. With the prototype demonstrations and simulations, AVTCT has the potential to overcome the control challenges with AVs and can facilitate AV reaching their full potential. Possible functionalities, benefits as well as challenges of AVTCT are discussed, which set the foundation for the conceptual model, simulation and real application of AVTCT.

Keywords: automated vehicle, connectivity and automation, intelligent transport system, traffic control, traffic safety

Procedia PDF Downloads 120

Authors: Maria Lucia G. Lourenco, Viviane Y. Hibaru, Keylla H. N. P. Pereira, Fabiana F. Souza, Joao C. P. Ferreira, Simone B. Chiacchio, Luiz H. A. Machado

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Isosporiasis is an affliction caused by coccidial protozoa belonging to genera Isospora spp. or Cystoisospora spp., which may parasitize the small and large intestines of dogs, of which neonates and young animals present higher risk of infection. This study aims at reporting a case of isosporiasis in neonate Pitbull dogs, as well as the diagnosis and treatment. Seven Pitbull puppies were admitted to the São Paulo State University (UNESP) Veterinary Hospital, Botucatu, São Paulo, Brazil, with history of yellowish diarrhea without mucus or blood for the past two days. The animals were five days old. The history of the mother, a primiparous two-year-old, revealed that she was properly vaccinated, not de-wormed and did not present diarrhea. The clinical examination revealed that the neonates weighted between 308 and 360 grams, and presented normal reflexes, moderate dehydration, body temperatures between 36.8 and 37.2 ºC, blood sugar between 103 and 124 mg/dL and normal appetite. A full blood count and a parasitology assay were performed to aid in the diagnosis. The full blood count detected eosinophilia, without any other relevant alterations. The parasitology assay (Willis-Molly & Faust) revealed the presence of Cystoisospora spp. The treatment was instituted with heated fluid therapy with Ringer’s Lactate (4 mL/100 g, subcutaneous) and antibiotic therapy with sulfamethoxazole-trimethoprim (15 mg/kg, orally) every 12 hours for ten days. The mother and other dogs that came in contact with the newborns were also treated. The environment was disinfected for 10 minutes with 1.6% quaternary ammonium. After 10 days, the newborns presented normal clinical signs and no alterations in the full blood count. Isosporiasis is an affliction with high mortality rates in litters that should be diagnosed and treated as soon as possible to increase the survival rates in these patients.

Keywords: Cystoisospora spp., neonatal infection, puppies, diarrhea,

Procedia PDF Downloads 109

Authors: Najwa Mimouni, Omar Rahli, Rachid Bennacer, Salah Chikh

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In the present work 2D and 3D numerical simulations of double diffusion natural convection in an elongated enclosure filled with a binary fluid saturating a porous medium are carried out. In the formulation of the problem, the Boussinesq approximation is considered and cross Neumann boundary conditions are specified for heat and mass walls conditions. The numerical method is based on the control volume approach with the third order QUICK scheme. Full approximation storage (FAS) with full multigrid (FMG) method is used to solve the problem. For the explored large range of the controlling parameters, we clearly evidenced that the increase in the depth of the cavity i.e. the lateral aspect ratio has an important effect on the flow patterns. The 2D perfect parallel flows obtained for a small lateral aspect ratio are drastically destabilized by increasing the cavity lateral dimension. This yields a 3D fluid motion with a much more complicated flow pattern and the classically studied 2D parallel flows are impossible.

Keywords: bifurcation, natural convection, heat and mass transfer, parallel flow, porous media

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Authors: Aleksandra Majchrzak, Katarzyna Baruch, Monika Sobolewska, Bartlomiej Chojnacki, Adam Pilch

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Scaled modeling is very common in the areas of science such as aerodynamics or fluid mechanics, since defining characteristic numbers enables to determine relations between objects under test and their models. In acoustics, scaled modeling is aimed mainly at investigation of room acoustics, sound insulation and sound absorption phenomena. Despite such a range of application, there is no method developed that would enable scaling acoustical perforated panels freely, maintaining their sound absorption coefficient in a desired frequency range. However, conducted theoretical and numerical analyses have proven that it is not physically possible to obtain given sound absorption coefficient in a desired frequency range by directly scaling only all of the physical dimensions of a perforated panel, according to a defined characteristic number. This paper is a continuation of the research mentioned above and presents practical evaluation of theoretical and numerical analyses. The measurements of sound absorption coefficient of perforated panels were performed in order to verify previous analyses and as a result find the relations between full-scale perforated panels and their models which will enable to scale them properly. The measurements were conducted in a one-to-eight model of a reverberation chamber of Technical Acoustics Laboratory, AGH. Obtained results verify theses proposed after theoretical and numerical analyses. Finding the relations between full-scale and modeled perforated panels will allow to produce measurement samples equivalent to the original ones. As a consequence, it will make the process of designing acoustical perforated panels easier and will also lower the costs of prototypes production. Having this knowledge, it will be possible to emulate in a constructed model panels used, or to be used, in a full-scale room more precisely and as a result imitate or predict the acoustics of a modeled space more accurately.

Keywords: characteristic numbers, dimensional analysis, model study, scaled modeling, sound absorption coefficient

Procedia PDF Downloads 179

Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: Brayden Mi

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Reverse time migration has been widely used in the Petroleum exploration industry to reveal subsurface images and to detect rock and fluid properties since the early 1980s. The seismic technology involves the construction of a velocity model through interpretive model construction, seismic tomography, or full waveform inversion, and the application of the reverse-time propagation of acquired seismic data and the original wavelet used in the acquisition. The methodology has matured from 2D, simple media to present-day to handle full 3D imaging challenges in extremely complex geological conditions. Conventional Ultrasound computed tomography (USCT) utilize travel-time-inversion to reconstruct the velocity structure of an organ. With the velocity structure, USCT data can be migrated with the “bend-ray” method, also known as migration. Its seismic application counterpart is called Kirchhoff depth migration, in which the source of reflective energy is traced by ray-tracing and summed to produce a subsurface image. It is well known that ray-tracing-based migration has severe limitations in strongly heterogeneous media and irregular acquisition geometries. Reverse time migration (RTM), on the other hand, fully accounts for the wave phenomena, including multiple arrives and turning rays due to complex velocity structure. It has the capability to fully reconstruct the image detectable in its acquisition aperture. The RTM algorithms typically require a rather accurate velocity model and demand high computing powers, and may not be applicable to real-time imaging as normally required in day-to-day medical operations. However, with the improvement of computing technology, such a computational bottleneck may not present a challenge in the near future. The present-day (RTM) algorithms are typically implemented from a flat datum for the seismic industry. It can be modified to accommodate any acquisition geometry and aperture, as long as sufficient illumination is provided. Such flexibility of RTM can be conveniently implemented for the application in USCT imaging if the spatial coordinates of the transmitters and receivers are known and enough data is collected to provide full illumination. This paper proposes an implementation of a full 3D RTM algorithm for USCT imaging to produce an accurate 3D acoustic image based on the Phase-shift-plus-interpolation (PSPI) method for wavefield extrapolation. In this method, each acquired data set (shot) is propagated back in time, and a known ultrasound wavelet is propagated forward in time, with PSPI wavefield extrapolation and a piece-wise constant velocity model of the organ (breast). The imaging condition is then applied to produce a partial image. Although each image is subject to the limitation of its own illumination aperture, the stack of multiple partial images will produce a full image of the organ, with a much-reduced noise level if compared with individual partial images.

Keywords: illumination, reverse time migration (RTM), ultrasound computed tomography (USCT), wavefield extrapolation

Procedia PDF Downloads 55

Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: bacteria chromosome, bacterial identification, sequence, primer generation

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Authors: Vilma Sasyte, Vilma Viliene, Agila Dauksiene, Asta Raceviciute-Stupeliene, Romas Gruzauskas, Saulius Alijosius

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The eight-week feeding trial was conducted involving 27-wk-old Isa brown laying hens to study the effect of dry extrusion processing on partial reduction in total glucosinolates content of locally produced rapeseed and on productivity and eggs quality parameters of laying hens. Thirty-six hens were randomly assigned one of three treatments (CONTR, AERS and HERS), each comprising 12, individual caged layers. The main composition of the diets was the same, but extruded soya bean seed were replaced with 2.5% of the extruded rapeseed in the AERS group and 4.5 % in the HERS group. Rapeseed was extruded together with faba beans. Due to extrusion process the glucosinolates content was reduced by 7.83 µmol/g of rapeseed. The results of conducted trial shows, that during all experimental period egg production parameters, such as the average feed intake (6529.17 vs. 6257 g/hen/14 day; P < 0.05) and laying intensity (94.35% vs. 89.29; P < 0.05) were statistically different for HERS and CONTR laying hens respectively. Only the feed conversion ratio to produce 1 kg of eggs, kg in AERS group was by 11 % lower compared to CONTR group (P < 0.05). By analysing the effect of extruded rapeseed on egg mass, the statistical differences between treatments were no determined. The dietary treatments did not affect egg weight, albumen height, haugh units, albumen and yolk pH. However, in the HERS group were get eggs with the more intensive yolk color, higher redness (a) and yellowness (b) values. The inclusion of full-fat extruded rapeseed had no effect on egg shell quality parameters, i.e. shell breaking strength, shell weight with and without coat and shell index, but in the experimental groups were get eggs with the thinner shell (P < 0.05). The internal egg quality analysis showed that with higher content of extruded rapeseed (4.5 %) level in the diet, the total cholesterol in the eggs yolk decreased by 1.92 mg/g in comparison with CONTR group (P < 0.05). Eggs laid by hens fed the diet containing 2.5% and 4.5% had increasing ∑PNRR/∑SRR ratio and decreasing ∑(n-6)/∑(n-3) ratio values of eggs yolk fatty acids than in CONTR group. Eggs of hens fed different amount of extruded rapeseed presented an n-6 : n-3 ratio changed from 5.17 to 4.71. The analysis of the relationship between hypocholesteremia/ hypercholesterolemia fatty acids (H/H), which is based on the functional properties of fatty acids, found that the value of it ratio is significant higher in laying hens fed diets supplemented with 4.5% extruded rapeseed than the CONTR group, demonstrating the positive effects of extruded rapeseed on egg quality. The results of trial confirmed that extruded full fat rapeseed to the 4.5% are suitable to replace soyabean in the compound feed of laying hens.

Keywords: egg quality, extruded full-fat rapeseed, laying hens, productivity

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Authors: Jian-Jun Shu

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The statistical properties of CRMs are explored by estimating similar-word set occurrence distribution. It is observed that CRMs tend to have a fat-tail distribution for similar-word set occurrence. Thus, the fat-tail test with two fatness coefficients is proposed to distinguish CRMs from non-CRMs, especially from exons. For the first fatness coefficient, the separation accuracy between CRMs and exons is increased as compared with the existing content-based CRM prediction method – fluffy-tail test. For the second fatness coefficient, the computing time is reduced as compared with fluffy-tail test, making it very suitable for long sequences and large data-base analysis in the post-genome time. Moreover, these indexes may be used to predict the CRMs which have not yet been observed experimentally. This can serve as a valuable filtering process for experiment.

Keywords: statistical approach, transcription factor binding sites, cis-regulatory modules, DNA sequences

Procedia PDF Downloads 270

Authors: Ming-Hsiang Shih, Wen-Pei Sung, Shih-Heng Tung

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Semi-active control system for structure under excitation of earthquake provides with the characteristics of being adaptable and requiring low energy. DSHD (Displacement Semi-Active Hydraulic Damper) was developed by our research team. Shake table test results of this DSHD installed in full scale test structure demonstrated that this device brought its energy-dissipating performance into full play for test structure under excitation of earthquake. The objective of this research is to develop a new AIC (Active Interaction Control Device) and apply shake table test to perform its dissipation of energy capability. This new proposed AIC is converting an improved DSHD (Displacement Semi-Active Hydraulic Damper) to AIC with the addition of an accumulator. The main concept of this energy-dissipating AIC is to apply the interaction function of affiliated structure (sub-structure) and protected structure (main structure) to transfer the input seismic force into sub-structure to reduce the structural deformation of main structure. This concept is tested using full-scale multi-degree of freedoms test structure, installed with this proposed AIC subjected to external forces of various magnitudes, for examining the shock absorption influence of predictive control, stiffness of sub-structure, synchronous control, non-synchronous control and insufficient control position. The test results confirm: (1) this developed device is capable of diminishing the structural displacement and acceleration response effectively; (2) the shock absorption of low precision of semi-active control method did twice as much seismic proof efficacy as that of passive control method; (3) active control method may not exert a negative influence of amplifying acceleration response of structure; (4) this AIC comes into being time-delay problem. It is the same problem of ordinary active control method. The proposed predictive control method can overcome this defect; (5) condition switch is an important characteristics of control type. The test results show that synchronism control is very easy to control and avoid stirring high frequency response. This laboratory results confirm that the device developed in this research is capable of applying the mutual interaction between the subordinate structure and the main structure to be protected is capable of transforming the quake energy applied to the main structure to the subordinate structure so that the objective of minimizing the deformation of main structural can be achieved.

Keywords: DSHD (Displacement Semi-Active Hydraulic Damper), AIC (Active Interaction Control Device), shake table test, full scale structure test, sub-structure, main-structure

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Authors: Fayzan Ahmed, Saad Bin Saeed, Abdul Qadir Jangda

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Gafchromic™ sheet are extensively used for the QA of intensity modulated radiation therapy and other in-vivo dosimetry. Intra-sheet Non-uniformity of scanner as well as film causes undesirable fluctuations which are reflected in dosimetry The aim of this study is to define a systematic and robust method to investigate the intra-sheet uniformity of the unexposed Gafchromic Sheets and the region of interest (ROI) of the scanner. Sheets of lot No#: A05151201 were scanned before and after the expiry period with the EPSON™ XL10000 scanner in the transmission mode, landscape orientation and 72 dpi resolution. ROI of (8’x 10’ inches) equal to the sheet dimension in the center of the scanner is used to acquire images with full transmission, block transmission and with sheets in place. 500 virtual grids, created in MATALB® are imported as a macros in ImageJ (1.49m Wayne Rasband) to analyze the images. In order to remove the edge effects, the outer 86 grids are excluded from the analysis. The standard deviation of the block transmission and full transmission are 0.38% and 0.66% confirming a higher uniformity of the scanner. Expired and non-expired sheets have standard deviations of 2.18% and 1.29%, show that uniformity decreases after expiry. The results are promising and indicates a good potential of this method to be used as a uniformity check for scanner and unexposed Gafchromic sheets.

Keywords: IMRT, film dosimetry, virtual grids, uniformity

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Authors: H. Imad, Y. Cheah, O. Aamera

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The aims of this research are to study the mitochondrial non-coding region by using the Sanger sequencing technique and establish the degree of variation characteristics of a fragment. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. A portion of a non-coding region encompassing positions 37 to 340 amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column then sequenced and detected by using the ABI 3730xL DNA Analyzer. New polymorphic positions 57, 63, and 101 are described may in future be suitable sources for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence most promising for identification variants.

Keywords: encompassing nucleotide positions 37 to 340, HVII, Iraq, mitochondrial DNA, polymorphism, frequency

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Authors: Foluke Abimbola

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The United Nations Convention on the rights of the child has been signed and ratified by several countries due to the concern about various abuses and crimes committed against children both locally and internationally. It is a shame that in view of the peculiar hardships being experienced by children today, the natural right to childhood has to be protected by a vast array of laws and international conventions. 194 countries have so far acceded to and ratified the convention on the Rights of a Child while some countries such as Nigeria have enacted the convention as a domestic law, yet child abuse is still rampant not only in Nigeria but all over the world. In Nigeria, the Child Rights Act was passed into law in 2003, with its provisions similar to the United Nations Convention on the Rights of a Child. Despite the age of marriage provided in the Nigerian Child’s Rights Act 2003, many communities still practice child marriages to the detriment of the girl-child. Cases where these children have to withdraw from school as a result of these unripe marriages abound. Unfortunately, the Constitution of the Federal Republic of Nigeria 1999 appears to indirectly support early marriages for girls in section 29 (4) where it states that a woman who is married is deemed to be of full age whereas ‘full age’ as a general term in the Constitution is from 18 years old and above. Section 29 (4) may thus be interpreted to mean that a girl of 12 years old, if married, is deemed to be of ‘full-age.’ In view of these discrepancies which continue to justify this unwholesome practice, this paper shall proffer solutions to this unlawful act and make recommendations to existing institutions, using a rights-based approach, on how to prevent and/or substantially reduce this practice. A comparative analysis with other African countries will be adopted in order to conduct a research for effective policies that may be implemented for the protection of these girls. Thus, this paper will further examine the issue of child marriage which is still quite rampant in African countries particularly in Nigeria which also affects the girl-child’s right to an education. Such children are in need of special protection and this paper will recommend ways in which state institutions, particularly in Nigeria, may be able to introduce policies to curb incidences of child marriage and child sexual abuse while proffering strategies for the prevention of these crimes.

Keywords: child abuse, child marriages, child rights, constitutions, child rights, the girl-child

Procedia PDF Downloads 121

Authors: N. C. van der Merwe, J. Oosthuizen, M. F. Makhetha, J. Adams, B. K. Dajee, S-R. Schneider

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Women representing high-risk breast cancer families, who tested negative for pathogenic mutations in BRCA1 and BRCA2, are four times more likely to develop breast cancer compared to women in the general population. Sequencing of genes involved in genomic stability and DNA repair led to the identification of novel contributors to familial breast cancer risk. These include BLM and PALB2. Bloom's syndrome is a rare homozygous autosomal recessive chromosomal instability disorder with a high incidence of various types of neoplasia and is associated with breast cancer when in a heterozygous state. PALB2, on the other hand, binds to BRCA2 and together, they partake actively in DNA damage repair. Archived DNA samples of 66 BRCA1/2 negative high-risk breast cancer patients were retrospectively selected based on the presence of an extensive family history of the disease ( > 3 affecteds per family). All coding regions and splice-site boundaries of both genes were screened using High-Resolution Melting Analysis. Samples exhibiting variation were bi-directionally automated Sanger sequenced. The clinical significance of each variant was assessed using various in silico and splice site prediction algorithms. Comprehensive screening identified a total of 11 BLM and 26 PALB2 variants. The variants detected ranged from global to rare and included three novel mutations. Three BLM and two PALB2 likely pathogenic mutations were identified that could account for the disease in these extensive breast cancer families in the absence of BRCA mutations (BLM c.11T > A, p.V4D; BLM c.2603C > T, p.P868L; BLM c.3961G > A, p.V1321I; PALB2 c.421C > T, p.Gln141Ter; PALB2 c.508A > T, p.Arg170Ter). Conclusion: The study confirmed the contribution of pathogenic mutations in BLM and PALB2 to the familial breast cancer burden in South Africa. It explained the presence of the disease in 7.5% of the BRCA1/2 negative families with an extensive family history of breast cancer. Segregation analysis will be performed to confirm the clinical impact of these mutations for each of these families. These results justify the inclusion of both these genes in a comprehensive breast and ovarian next generation sequencing cancer panel and should be screened simultaneously with BRCA1 and BRCA2 as it might explain a significant percentage of familial breast and ovarian cancer in South Africa.

Keywords: Bloom Syndrome, familial breast cancer, PALB2, South Africa

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

Procedia PDF Downloads 253

Authors: Fayzan Ahmed, Saad Bin Saeed, Abdul Qadir Jangda

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Gafchromic™ sheet are extensively used for the QA of intensity modulated radiation therapy and other in-vivo dosimetry. Intra-sheet Non-uniformity of scanner as well as film causes undesirable fluctuations which are reflected in dosimetry The aim of this study is to define a systematic and robust method to investigate the intra-sheet uniformity of the unexposed Gafchromic Sheets and the region of interest (ROI) of the scanner. Sheets of lot No#: A05151201 were scanned before and after the expiry period with the EPSON™ XL10000 scanner in the transmission mode, landscape orientation, and 72 dpi resolution. ROI of (8’x 10’ inches) equal to the sheet dimension in the center of the scanner is used to acquire images with full transmission, block transmission and with sheets in place. 500 virtual grids, created in MATALB® are imported as a macros in ImageJ (1.49m Wayne Rasband) to analyze the images. In order to remove the edge effects, the outer 86 grids are excluded from the analysis. The standard deviation of the block transmission and full transmission are 0.38% and 0.66% confirming a higher uniformity of the scanner. Expired and non-expired sheets have standard deviations of 2.18% and 1.29%, show that uniformity decreases after expiry. The results are promising and indicate a good potential of this method to be used as a uniformity check for scanner and unexposed Gafchromic sheets.

Keywords: IMRT, film dosimetry, virtual grids, uniformity

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Authors: Rachel Danielson, Brendan Bohannan, S.M. Tsai, Kyle Meyer, Jorge L.M. Rodrigues

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The Amazon Rainforest is a global diversity hotspot and crucial carbon sink, but approximately 20% of its total extent has been deforested- primarily for the establishment of cattle pasture. Understanding the impact of this large-scale disturbance on soil microbial community composition and activity is crucial in understanding potentially consequential shifts in nutrient or greenhouse gas cycling, as well as adding to the body of knowledge concerning how these complex communities respond to human disturbance. In this study, surface soils (0-10cm) were collected from three forests and three 45-year-old pastures in Rondonia, Brazil (the Amazon state with the greatest rate of forest destruction) in order to determine the impact of forest conversion on microbial communities involved in nitrogen fixation. Soil chemical and physical parameters were paired with measurements of microbial activity and genetic profiles to determine how community composition and process rates relate to environmental conditions. Measuring both the natural abundance of 15N in total soil N, as well as incorporation of enriched 15N2 under incubation has revealed that conversion of primary forest to cattle pasture results in a significant increase in the rate of nitrogen fixation by free-living diazotrophs. Quantification of nifH gene copy numbers (an essential subunit encoding the nitrogenase enzyme) correspondingly reveals a significant increase of genes in pasture compared to forest soils. Additionally, genetic sequencing of both nifH genes and transcripts shows a significant increase in the diversity of the present and metabolically active diazotrophs within the soil community. Levels of both organic and inorganic nitrogen tend to be lower in pastures compared to forests, with ammonium rather than nitrate as the dominant inorganic form. However, no significant or consistent differences in total, extractable, permanganate-oxidizable, or loss-on-ignition carbon are present between the two land-use types. Forest conversion is associated with a 0.5- 1.0 unit pH increase, but concentrations of many biologically relevant nutrients such as phosphorus do not increase consistently. Increases in free-living diazotrophic community abundance and activity appear to be related to shifts in carbon to nitrogen pool ratios. Furthermore, there may be an important impact of transient, low molecular weight plant-root-derived organic carbon on free-living diazotroph communities not captured in this study. Preliminary analysis of nitrogenase gene variant composition using NovoSeq metagenomic sequencing indicates that conversion of forest to pasture may significantly enrich vanadium-based nitrogenases. This indication is complemented by a significant decrease in available soil molybdenum. Very little is known about the ecology of diazotrophs utilizing vanadium-based nitrogenases, so further analysis may reveal important environmental conditions favoring their abundance and diversity in soil systems. Taken together, the results of this study indicate a significant change in nitrogen cycling and diazotroph community composition with the conversion of the Amazon Rainforest. This may have important implications for the sustainability of cattle pastures once established since nitrogen is a crucial nutrient for forage grass productivity.

Keywords: free-living diazotrophs, land use change, metagenomic sequencing, nitrogen fixation

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Authors: Busra Mutlu Ipek, Merve Mutlu, Ahmet Mutlu

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Novel coronavirus COVID-19, which has recently influenced the world, poses a great threat to humanity. In order to overcome this challenging situation, scientists are working on developing effective vaccine against coronavirus. Many experts and researchers have also produced articles and done studies on this highly important subject. In this direction, this special topic was chosen for article to make a contribution to this area. The purpose of this article is to perform RNA sequence analysis of selected virus forms in the Coronaviridae family and predict/classify SARS-CoV-2 (COVID-19) from other selected complete genomes in coronaviridae family using proposed Artificial Neural Network(ANN) algorithm.

Keywords: Coronaviridae family, COVID-19, RNA sequencing, ANN, neural network

Procedia PDF Downloads 128

Authors: Chi T. L. Pham, L. Vu, Hoang T. Le, Huong T. T. Le, Quyen T. T. Bui

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Burning joss paper and incense during religious and cultural ceremonies is common in Vietnam. This study aims to measure the impact of burning joss paper and incense during Vu Lai festival (full moon of July) in Vietnam. Data of Hanoi air quality in year 2020 was used. Interrupted time series analysis was employed to examine the changes in pattern of various air quality indicators before and after the festival period. The results revealed that burning joss paper and incense led to an immediate increase of 15.94 units in the air quality index on the first day, which gradually rose to 47.4 units by the end of the full moon period. Regarding NO2, PM10, and PM25, there was no significant immediate change at the start of the intervention period (August 29th, 2020). However, significant increases in levels and an upward trend were observed during the intervention time, followed by substantial decreases after the intervention period ended (September 3rd, 2020). This analysis did not find a significant impact on CO, SO2, and O3 due to burning joss paper and incense. These findings provide valuable insights for policymakers and stakeholders involved in managing and enhancing air quality in regions where such practices are prevalent.

Keywords: air pollution, incense, ITSA, joss paper, religious activities

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Authors: Heeba A. Gurku

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Introduction: Cone Beam CT(CBCT) images play an integral part in proper patient positioning in cancer patients undergoing radiation therapy treatment. But these images are low in quality. The purpose of this study is to generate high-quality synthetic CT images from CBCT using generative models. Material and Methods: This study utilized two datasets from The Cancer Imaging Archive (TCIA) 1) Lung cancer dataset of 20 patients (with full view CBCT images) and 2) Pancreatic cancer dataset of 40 patients (only 27 patients having limited view images were included in the study). Cycle Generative Adversarial Networks (GAN) and its variant Attention Guided Generative Adversarial Networks (AGGAN) models were used to generate the synthetic CTs. Models were evaluated by visual evaluation and on four metrics, Structural Similarity Index Measure (SSIM), Peak Signal Noise Ratio (PSNR) Mean Absolute Error (MAE) and Root Mean Square Error (RMSE), to compare the synthetic CT and original CT images. Results: For pancreatic dataset with limited view CBCT images, our study showed that in Cycle GAN model, MAE, RMSE, PSNR improved from 12.57to 8.49, 20.94 to 15.29 and 21.85 to 24.63, respectively but structural similarity only marginally increased from 0.78 to 0.79. Similar, results were achieved with AGGAN with no improvement over Cycle GAN. However, for lung dataset with full view CBCT images Cycle GAN was able to reduce MAE significantly from 89.44 to 15.11 and AGGAN was able to reduce it to 19.77. Similarly, RMSE was also decreased from 92.68 to 23.50 in Cycle GAN and to 29.02 in AGGAN. SSIM and PSNR also improved significantly from 0.17 to 0.59 and from 8.81 to 21.06 in Cycle GAN respectively while in AGGAN SSIM increased to 0.52 and PSNR increased to 19.31. In both datasets, GAN models were able to reduce artifacts, reduce noise, have better resolution, and better contrast enhancement. Conclusion and Recommendation: Both Cycle GAN and AGGAN were significantly able to reduce MAE, RMSE and PSNR in both datasets. However, full view lung dataset showed more improvement in SSIM and image quality than limited view pancreatic dataset.

Keywords: CT images, CBCT images, cycle GAN, AGGAN

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Authors: Laura G. Caixeta, Maico R. Severino

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One of the biggest challenges that the industries find nowadays is to incorporate sustainability practices into its operations. The Green Supply Chain Management (GSCM) concept assists industries in such incorporation. For the full application of this concept is important that enterprises of a same supply chain have the GSCM practices coordinated among themselves. Note that this type of analyses occurs on the context of developed countries and sectors considered big impactors (as automotive, mineral, among others). The propose of this paper is to analyze as the GSCM concepts are applied on the Brazilian animal nutrition industries. The method used was the Case Study. For this, it was selected a supply chain relationship composed by animal nutrition products manufacturer (Enterprise A) and its supplier of animal waste, such as blood, viscera, among others (Enterprise B). First, a literature review was carried out to identify the main GSCM practices. Second, it was done an individual analysis of each one selected enterprise of the application of GSCM concept. For the observed practices, the coordination of each practice in this supply chain was studied. And, it was developed propose of GSCM applications for the practices no observed. The findings of this research were: a) the systematization of main GSCM practices, as: Internal Environment Management, Green Consumption, Green Design, Green Manufacturing, Green Marketing, Green Packaging, Green Procurement, Green Recycling, Life Cycle Analysis, Consultation Selection Method, Environmental Risk Sharing, Investment Recovery, and Reduced Transportation Time; b) the identification of GSCM practices on Enterprise A (7 full application, 3 partial application and 3 no application); c) the identification of GSCM practices on Enterprise B (2 full application, 2 partial application and 9 no application); d) the identification of how is the incentive and the coordination of the GSCM practices on this relationship by Enterprise A; e) proposals of application and coordination of the others GSCM practices on this supply chain relationship. Based on the study, it can be concluded that its possible apply GSCM on animal nutrition industries, and when occurs the motivation on the application of GSCM concepts by a supply chain echelon, these concepts are deployed for the others supply chain echelons by the coordination (orchestration) of the first echelon.

Keywords: animal nutrition industries, coordination, green supply chain management, supply chain management, sustainability

Procedia PDF Downloads 113

Authors: John G. Skelly, Peter K. Dearden, Thomas W. R. Harrop, Sarah N. Inwood, Joseph Guhlin

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The Argentine stem weevil (ASW; L. bonariensis) is an economically important pasture pest in New Zealand, which causes about $200 million of damage per annum. Microctonus hyperodae (Mh), a parasite of the ASW in its natural range in South America, was introduced into New Zealand to curb the pasture damage caused by the ASW. Mh is an endoparasitic wasp that lays its eggs in the ASW halting its reproduction. Mh was initially successful at preventing ASW proliferation and reducing pasture damage. The effectiveness of Mh has since declined due to decreased parasitism rates and has resulted in increased pasture damage. Although the mechanism through which ASW has developed resistance to Mh has not been discovered, it has been proposed to be due to the different reproductive modes used by Mh and the ASW in New Zealand. The ASW reproduces sexually, whereas Mh reproduces asexually, which has been hypothesised to have allowed the ASW to ‘out evolve’ Mh. Other species within the Microctonus genus reproduce both sexually and asexually. Strains of Microctonus aethiopoides (Ma), a species closely related to Mh, reproduce either by sexual or asexual reproduction. Comparing the genomes of sexual and asexual Microctonus may allow for the identification of the mechanism of asexual reproduction and other characteristics that may improve Mh as a biocontrol agent. The genomes of Mh and three strains of Ma, two of which reproduce sexually and one reproduces asexually, have been sequenced and annotated. The French (MaFR) and Moroccan (MaMO) reproduce sexually, whereas the Irish strain (MaIR) reproduces asexually. Like Mh, The Ma strains are also used as biocontrol agents, but for different weevil species. The genomes of Mh and MaIR were subsequently upgraded using Hi-C, resulting in a set of high quality, highly contiguous genomes. A subset of the genes involved in mitosis and meiosis, which have been identified though the use of Hidden Markov Models generated from genes involved in these processes in other Hymenoptera, have been catalogued in Mh and the strains of Ma. Meiosis and mitosis genes were broadly conserved in both sexual and asexual Microctonus species. This implies that either the asexual species have retained a subset of the molecular components required for sexual reproduction or that the molecular mechanisms of mitosis and meiosis are different or differently regulated in Microctonus to other insect species in which these mechanisms are more broadly characterised. Bioinformatic analysis of the chemoreceptor compliment in Microctonus has revealed some variation in the number of olfactory receptors, which may be related to host preference. Phylogenetic analysis of olfactory receptors highlights variation, which may be able to explain different host range preferences in the Microctonus. Hi-C clustering implies that Mh has 12 chromosomes, and MaIR has 8. Hence there may be variation in gene regulation between species. Genome alignment of Mh and MaIR implies that there may be large scale genome structural variation. Greater insight into the genetics of these agriculturally important group of parasitic wasps may be beneficial in restoring or maintaining their biocontrol efficacy.

Keywords: argentine stem weevil, asexual, genomics, Microctonus hyperodae

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Authors: M. O. Bayram, H. B. Gencdal, N. O. Fercan, B. Basbug

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Liquid limit, which is used as a measure of soil strength, can be detected by Casagrande and fall-cone testing methods. The two methods majorly diverge from each other in terms of operator dependency. The Casagrande method that is applied according to ASTM D4318-17 standards may give misleading results, especially if the calibration process is not performed well. To reveal the effect of calibration for drop height and amount of soil paste placement in the Casagrande cup, a series of tests were carried out by multipoint method as it is specified in the ASTM standards. The tests include the combination of 6 mm, 8 mm, 10 mm, and 12 mm drop heights and under-filled, half-filled, and full-filled Casagrande cups by kaolinite samples. It was observed that during successive tests, the drop height of the cup deteriorated; hence the device was recalibrated before and after each test to provide the accuracy of the results. Besides, the tests by under-filled and full-filled samples for higher drop heights revealed lower liquid limit values than the lower drop heights revealed. For the half-filled samples, it was clearly seen that the liquid limit values didn’t change at all as the drop height increased, and this explains the function of standard specifications.

Keywords: calibration, casagrande cup method, drop height, kaolinite, liquid limit, placing form

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Authors: Pierre van Tonder, Christoff Kruger

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Modular concrete elements are used for retaining walls to provide lateral support. Depending on the retaining wall layout, these precast panels may be interlocking and may be tied into the soil backfill via geosynthetic strips. This study investigates the ultimate pull-out load increase, which is possible by adding varied diameter supplementary reinforcement through embedded anchor loops within concrete retaining wall panels. Full-scale panels used in practice have four embedded anchor points. However, only one anchor loop was embedded in the center of the experimental panels. The experimental panels had the same thickness but a smaller footprint (600mm x 600mm x 140mm) area than the full-sized panels to accommodate the space limitations of the laboratory and experimental setup. The experimental panels were also cast without any bending reinforcement as would typically be obtained in the full-scale panels. The exclusion of these reinforcements was purposefully neglected to evaluate the impact of a single bar reinforcement through the center of the anchor loops. The reinforcement bars had of 8 mm, 10 mm, 12 mm, and 12 mm. 30 samples of concrete panels with embedded anchor loops were tested. The panels were supported on the edges and the anchor loops were subjected to an increasing tensile force using an Instron piston. Failures that occurred were loop failures and panel failures and a mixture thereof. There was an increase in ultimate load vs. increasing diameter as expected, but this relationship persisted until the reinforcement diameter exceeded 10 mm. For diameters larger than 10 mm, the ultimate failure load starts to decrease due to the dependency of the reinforcement bond strength to the concrete matrix. Overall, the reinforced panels showed a 14 to 23% increase in the factor of safety. Using anchor loops of 66kN ultimate load together with Y10 steel reinforcement with bent ends had shown the most promising results in reducing concrete panel pull-out failure. The Y10 reinforcement had shown, on average, a 24% increase in ultimate load achieved. Previous research has investigated supplementary reinforcement around the anchor loops. This paper extends this investigation by evaluating supplementary reinforcement placed through the panel anchor loops.

Keywords: supplementary reinforcement, anchor loops, retaining panels, reinforced concrete, pull-out failure

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Authors: Danny Barash

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Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is that many are found in prokaryotes but only a small percentage of known riboswitches have been found in certain eukaryotic organisms. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods that include some slight structural considerations. These pattern-matching methods were the first ones to be applied for the purpose of riboswitch detection and they can also be programmed very efficiently using a data structure called affix arrays, making them suitable for genome-wide searches of riboswitch patterns. However, they are limited by their ability to detect harder to find riboswitches that deviate from the known patterns. Several methods have been developed since then to tackle this problem. The most commonly used by practitioners is Infernal that relies on Hidden Markov Models (HMMs) and Covariance Models (CMs). Profile Hidden Markov Models were also carried out in the pHMM Riboswitch Scanner web application, independently from Infernal. Other computational approaches that have been developed include RMDetect by the use of 3D structural modules and RNAbor that utilizes Boltzmann probability of structural neighbors. We have tried to incorporate more sophisticated secondary structure considerations based on RNA folding prediction using several strategies. The first idea was to utilize window-based methods in conjunction with folding predictions by energy minimization. The moving window approach is heavily geared towards secondary structure consideration relative to sequence that is treated as a constraint. However, the method cannot be used genome-wide due to its high cost because each folding prediction by energy minimization in the moving window is computationally expensive, enabling to scan only at the vicinity of genes of interest. The second idea was to remedy the inefficiency of the previous approach by constructing a pipeline that consists of inverse RNA folding considering RNA secondary structure, followed by a BLAST search that is sequence-based and highly efficient. This approach, which relies on inverse RNA folding in general and our own in-house fragment-based inverse RNA folding program called RNAfbinv in particular, shows capability to find attractive candidates that are missed by Infernal and other standard methods being used for riboswitch detection. We demonstrate attractive candidates found by both the moving-window approach and the inverse RNA folding approach performed together with BLAST. We conclude that structure-based methods like the two strategies outlined above hold considerable promise in detecting riboswitches and other conserved RNAs of functional importance in a variety of organisms.

Keywords: riboswitches, RNA folding prediction, RNA structure, structure-based methods

Procedia PDF Downloads 217